My thesis in LaTeX - needs pdflatex, minion pro and biber packages

thesis.tex

%!TEX TS-program = pdflatex
%!TEX encoding = UTF-8 Unicode

% Preamble (fold)
\documentclass[12pt, openright]{book}
% \includeonly{chapters/frontmatter, chapters/introduction}

% Load packages 
\usepackage[ibycus, english]{babel}
% \usepackage{amsmath, amssymb}
\usepackage[mathlf, textlf, loosequotes]{MinionPro}
\usepackage[top=2.3cm, left=4cm, right=2.3cm, bottom=2.3cm, a4paper]{geometry}
\usepackage[medium, compact]{titlesec}
\usepackage[authordate, hyperref, labelyear, natbib, uniquelist=minyear, uniquename=false, backend=biber]{biblatex-chicago}
\usepackage[svgnames]{xcolor} 
\usepackage[colorlinks, pdfborder={0 0 0}]{hyperref}     
\usepackage[font={small}, labelfont={color=DarkRed,bf}, labelsep=endash]{caption}
\usepackage{appendix, booktabs, csquotes, fancyhdr, footmisc, graphicx, lettrine, longtable, parskip, rotating, setspace, sidecap, tabularx, titletoc, microtype, wasysym}

% Settings
\hypersetup{pdfauthor={Jesse Robertson},
	pdftitle={Rheological controls on the dynamics of lava flow emplacement},
	pdfsubject={volcanology, rheology},
    colorlinks=false,
	bookmarksnumbered=true} % Set hyperref options 
\addbibresource{thesis.bib} % Set bibliography file 
\urlstyle{same} 
\setlength{\defaultaddspace}{10pt}
\renewcommand*{\footnotelayout}{\small}

% Some new macros
\newcommand{\degree}{\ensuremath{^{\circ}}}
\newcommand{\degreesC}{\ensuremath{^{\circ}\mbox{C}}}
\newcommand{\dd}{\ensuremath{\,\mathrm{d}}}
\newlength{\figurewidth}
\setlength{\figurewidth}{\textwidth}

% Page setup      
\pagestyle{fancy}
\renewcommand{\headrulewidth}{\iffloatpage{0pt}{0.0pt}}   
\setlength{\headheight}{15pt}
\renewcommand{\footrulewidth}{0pt}  
\renewcommand{\chaptermark}[1]{\markboth{\lowercase{\textssc{#1}}}{}} 
\renewcommand{\sectionmark}[1]{\markright{\lowercase{\textssc{#1}}}}
\fancyhead[LE,RO]{\thepage} 
\fancyhead[LO]{\rightmark} 
\fancyhead[RE]{\leftmark} 
\lfoot{}
\cfoot{} 
\rfoot{}

% Titling
\titleformat{\part}[display]{\color{DarkRed}\Huge\bf\centering}{}{1em}{}
\titleformat{\chapter}[display]{\color{DarkRed}\Large\bf}{\chaptertitlename\ \thechapter}{1em}{}
\titleformat{\section}{\color{DarkRed}\large\bf}{\thesection}{1em}{}
\titlespacing{\section}{0pt}{*2.0}{*0.2}
\titleformat{\subsection}{\color{darkgray}\normalsize\bf}{\thesubsection}{1em}{}
\titlespacing{\subsection}{0pt}{*1}{*0.2}
\titleformat{\subsubsection}{\color{darkgray}\normalsize\bf}{\thesubsubsection}{1em}{}
\titlespacing{\subsubsection}{0pt}{*0.2}{*0.2}               

% Define new commands for tabularx so that extendable centered, left-aligned and right-aligned can be used as well as columns of the type p{...}. These new definitions are based on solumns oc the type X combined with a format command, which saved typing it every time.
% The new definitions are: 
% 			X -> p{...}
% 			L -> left-aligned 
% 			Y -> centered 
% 			R -> right-aligned 
\newcolumntype{L}{>{\raggedright\arraybackslash}X} 
\newcolumntype{C}{>{\centering\arraybackslash}X} 
\newcolumntype{R}{>{\raggedleft\arraybackslash}X}
% Note that the commands above refer to the ragged side of the text, hence why left-aligned is ragged right and vice versa.

% \ChapterOutsidePart and \ChapterInsidePart: control the bookmark level of each
% sectioning command by renumbering
\makeatletter
\newcommand{\chapteroutsidepart}{
   \def\toclevel@chapter{-1}
   \def\toclevel@section{0}
   \def\toclevel@subsection{1}}
\newcommand{\chapterinsidepart}{
   \def\toclevel@chapter{0}
   \def\toclevel@section{1}
   \def\toclevel@subsection{2}}
\makeatother

% Define new comamnd for list of illustrations
\makeatletter
\providecommand\phantomsection{}% for hyperref

\newcommand\listofillustrations{%
    \chapter*{List of Illustrations}%
    \phantomsection
    \addcontentsline{toc}{chapter}{List of Illustrations}%
    \section*{Figures}%
    \phantomsection
    \addcontentsline{toc}{section}{\protect\numberline{}Figures}%
    \@starttoc{lof}%
    \bigskip
    \section*{Tables}%
    \phantomsection
    \addcontentsline{toc}{section}{\protect\numberline{}Tables}%
    \@starttoc{lot}}

\makeatother

% preamble (end)

\begin{document}

% \frenchspacing
\frontmatter
\include{chapters/frontmatter}
\singlespacing
\phantomsection \label{contents}
\addcontentsline{toc}{chapter}{Contents}
\tableofcontents
\listofillustrations         
\onehalfspacing
\newpage\newpage
\include{chapters/prologue}
\mainmatter 
\pagestyle{fancy}
\chapteroutsidepart
\include{chapters/introduction}

\chapterinsidepart
\part*{Isothermal flows}
\include{chapters/numerics}
\include{chapters/isothermal_results}
\include{chapters/isothermal_applications}

\part*{Cooling and solidifying flows}
\include{chapters/experiments}
\include{chapters/solidifying_results}
\include{chapters/solidifying_applications}

\chapteroutsidepart
\include{chapters/conclusions}

\backmatter
\fancyhead[RE]{\lowercase{\textssc{Notation}}} 
\fancyhead[LO]{\lowercase{\textssc{Notation}}}
\include{appendices/symbols_list}
\newpage
\fancyhead[RE]{\lowercase{\textssc{References}}} 
\fancyhead[LO]{\lowercase{\textssc{References}}}
\phantomsection \label{references}
\addcontentsline{toc}{chapter}{References}
\printbibliography[title=References]

\end{document}